Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 35 of 167
Found at i:10629918 original size:12 final size:13
Alignment explanation
Indices: 10629890--10629922 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10629880 TTATTTCTTT
10629890 TTCTCCATCTACC
1 TTCTCCATCTACC
*
10629903 TTCTCC-TCTTCC
1 TTCTCCATCTACC
10629915 TTCTCCAT
1 TTCTCCAT
10629923 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:10631022 original size:28 final size:28
Alignment explanation
Indices: 10630990--10631054 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
10630980 ATTTACTAGA
*
10630990 ATACCCCTATGTATGAAAAATTACCATT
1 ATACCCCTATGTATGAAAAATGACCATT
* * *
10631018 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGAAAAATGACCATT
10631046 ATACCCCTA
1 ATACCCCTA
10631055 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGAAAAATGACCATT
Found at i:10631221 original size:27 final size:28
Alignment explanation
Indices: 10631160--10631249 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
10631150 AGGAAGCGTC
*
10631160 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* * **
10631188 CTAGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
10631215 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
10631244 CTGGTG
1 CTGGTG
10631250 ACTCTGTCAC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
27 22 0.44
28 21 0.42
29 7 0.14
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:10631260 original size:29 final size:28
Alignment explanation
Indices: 10631170--10631260 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
10631160 CTGGTGGCTA
* * * *
10631170 TGCCACAAATTATCTGTTCTAGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
10631198 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
10631225 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
10631254 TGTCACA
1 TGCCACA
10631261 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.43
28 14 0.27
29 15 0.29
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:10631268 original size:55 final size:56
Alignment explanation
Indices: 10631160--10631274 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
10631150 AGGAAGCGTC
* * *
10631160 CTGGTGGCTATGCCACAAATTATCTGTTCTAGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTAGTGACCCTGCCACATATATCTGTAT
* * * *
10631215 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTAGTGACCCTGCCACATATATCTGTAT
10631271 CTGG
1 CTGG
10631275 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.60
56 19 0.38
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTAGTGACCCTGCCACATATATCTGTAT
Found at i:10631737 original size:19 final size:19
Alignment explanation
Indices: 10631713--10631751 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10631703 TTTTAATTAT
* *
10631713 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
10631732 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
10631751 T
1 T
10631752 ATGATGACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:10633945 original size:52 final size:52
Alignment explanation
Indices: 10633825--10633977 Score: 200
Period size: 52 Copynumber: 2.9 Consensus size: 52
10633815 CATATCATAT
* * *
10633825 CGATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCACAC
1 CGATGCCATAACCCAGCTATGGTCTTATACGGAAGCACA-TATCACATCACAC
* * * * **
10633878 AGATGCCATAGCCCAGCTATGGTCTTATAGGGGAA-CACGTATCACATTGCAC
1 CGATGCCATAACCCAGCTATGGTCTTATA-CGGAAGCACATATCACATCACAC
10633930 CGATGCCATAACCCAGCTATGGTCTTATACGGAAGCACATATCACATC
1 CGATGCCATAACCCAGCTATGGTCTTATACGGAAGCACATATCACATC
10633978 TTTTCCATCA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
51 4 0.05
52 49 0.57
53 29 0.34
54 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (52 bp):
CGATGCCATAACCCAGCTATGGTCTTATACGGAAGCACATATCACATCACAC
Found at i:10638255 original size:16 final size:16
Alignment explanation
Indices: 10638236--10638266 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10638226 CTTCTTCACT
10638236 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
10638252 TACTCACTTACTTAA
1 TACTCACTTACTTAA
10638267 TCAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:10638647 original size:55 final size:55
Alignment explanation
Indices: 10638510--10638820 Score: 312
Period size: 55 Copynumber: 5.7 Consensus size: 55
10638500 ATCCTTTTGA
* * *
10638510 AACTTACCATTGCCATGTCTTGACATGGTCTTTCATGGTATCC-TTGCCTTAT-G-
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGA-CCTTTGCCTTATAGT
* * *
10638563 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGT
* **** * *
10638618 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCC-T-TAGA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGT
* *
10638671 AACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
1 AA-CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGT
* **** * *
10638728 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCC-T-TAGA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGT
* *
10638781 AACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGG
1 AA-CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGG
10638821 TATCCTTAAA
Statistics
Matches: 211, Mismatches: 38, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
52 2 0.01
53 53 0.25
54 17 0.08
55 126 0.60
56 8 0.04
57 5 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (55 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:10638718 original size:110 final size:110
Alignment explanation
Indices: 10638510--10638820 Score: 529
Period size: 110 Copynumber: 2.8 Consensus size: 110
10638500 ATCCTTTTGA
* * * * * * *
10638510 AACTTACCATTGCCATGTCTTGACATGGTCTTTCATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTA-GAAACCTTACCAA
10638573 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
10638618 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTAGAAACCTTACCAAT
1 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTAGAAACCTTACCAAT
10638683 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
66 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
10638728 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTAGAAACCTTACCAAT
1 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTAGAAACCTTACCAAT
10638793 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
10638821 TATCCTTAAA
Statistics
Matches: 193, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
107 1 0.01
108 47 0.24
109 7 0.04
110 138 0.72
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (110 bp):
AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTAGAAACCTTACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:10638777 original size:165 final size:161
Alignment explanation
Indices: 10638508--10638819 Score: 387
Period size: 165 Copynumber: 1.9 Consensus size: 161
10638498 GTATCCTTTT
* * *
10638508 GAAACTTACCATTGCCATGTCTTGACATGGTCTTTCATGGTATCCTTGCCTTATGAACTCACCAA
1 GAAACTTACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAA
* * * * * *
10638573 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAA-CTTATCAA-TGCCATGT
66 TGCCATGCCTTGACATGGTCTTACATGAGACCATTGCC-T-TAGAAACCTTACCAATTGCCATGC
10638636 CTTGACATGGTCTTACATGATTTCATTGCCTTA
129 CTTGACATGGTCTTACATGATTTCATTGCCTTA
* *
10638669 GAAACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTT
1 GAAA-CTTACC-ATTGCCATGCCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTC
* * ***
10638733 ATCAATGCCATGTCTTGACATGGTCTTACATGATTTCATTGCCTTAGAAACCTTACCAATTGCCA
61 ACCAATGCCATGCCTTGACATGGTCTTACATGAGACCATTGCCTTAGAAACCTTACCAATTGCCA
*
10638798 TGCCTTGGCATGGTCTTACATG
126 TGCCTTGACATGGTCTTACATG
10638820 GTATCCTTAA
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
161 4 0.03
162 8 0.06
163 42 0.33
164 9 0.07
165 64 0.50
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (161 bp):
GAAACTTACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAA
TGCCATGCCTTGACATGGTCTTACATGAGACCATTGCCTTAGAAACCTTACCAATTGCCATGCCT
TGACATGGTCTTACATGATTTCATTGCCTTA
Found at i:10644363 original size:52 final size:52
Alignment explanation
Indices: 10644275--10644392 Score: 157
Period size: 52 Copynumber: 2.2 Consensus size: 52
10644265 ATCACATTAT
*
10644275 CACATTATCACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAA-
1 CACA-TATCACATCACACCGATGCCATAACCCAGCTATGGTCTTATAC-GGAAG
* ** * *
10644328 CACGTATCACATTGCACTGATGCCATAACCTAGCTATGGTCTTATACGGAAG
1 CACATATCACATCACACCGATGCCATAACCCAGCTATGGTCTTATACGGAAG
10644380 CACATATCACATC
1 CACATATCACATC
10644393 TTTTCCGTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 4 0.07
52 49 0.88
53 3 0.05
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (52 bp):
CACATATCACATCACACCGATGCCATAACCCAGCTATGGTCTTATACGGAAG
Found at i:10646088 original size:42 final size:43
Alignment explanation
Indices: 10646023--10646135 Score: 121
Period size: 41 Copynumber: 2.7 Consensus size: 43
10646013 ATATCGTACA
* *
10646023 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGC-TATCACATACG
1 ATGCC-ACTGTCCCAGACAG-GGTCTTACATGCAAATCAAATACG
10646065 ATGCCACTGTCCCAGACAGGGTCTTACA--CAAATCAAATACG
1 ATGCCACTGTCCCAGACAGGGTCTTACATGCAAATCAAATACG
* *
10646106 ATGTCGA-TGTCCCAGACATGGTCTTACATG
1 ATG-CCACTGTCCCAGACAGGGTCTTACATG
10646136 TAATCATAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
40 1 0.02
41 34 0.56
42 25 0.41
43 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACAGGGTCTTACATGCAAATCAAATACG
Found at i:10652703 original size:49 final size:49
Alignment explanation
Indices: 10652622--10653066 Score: 446
Period size: 49 Copynumber: 8.9 Consensus size: 49
10652612 GCTATTGTGA
* * *
10652622 GGTCACGTCTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
10652671 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA-TTCGTACCTGATAACTTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGT-GTACCAGATAA--TT
* * * * **
10652722 GATCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
** * *
10652771 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
10652821 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA-TTCGTACCTGATAACTTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGT-GTACCAGATAA--TT
* * * * **
10652872 GATCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTATCAGATGGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
** * *
10652921 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
10652971 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTA-TTCGTACCTGATAACTTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGT-GTACCAGATAA--TT
* * * *
10653022 GATCACGTGTGTAGTACTAAGTGCAGACTACTACGTGTATCAGAT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
10653067 GGTTCTCAGT
Statistics
Matches: 323, Mismatches: 59, Indels: 26
0.79 0.14 0.06
Matches are distributed among these distances:
48 3 0.01
49 121 0.37
50 82 0.25
51 114 0.35
52 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:10652892 original size:150 final size:150
Alignment explanation
Indices: 10652621--10653070 Score: 864
Period size: 150 Copynumber: 3.0 Consensus size: 150
10652611 AGCTATTGTG
* * * *
10652621 AGGTCACGTCTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
1 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
10652686 ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
66 ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
10652751 ACTACGTGTATCAGATGGTT
131 ACTACGTGTATCAGATGGTT
10652771 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
10652836 ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
66 ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
10652901 ACTACGTGTATCAGATGGTT
131 ACTACGTGTATCAGATGGTT
10652921 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
1 AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
10652986 ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
66 ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
10653051 ACTACGTGTATCAGATGGTT
131 ACTACGTGTATCAGATGGTT
10653071 CTCAGTAAAA
Statistics
Matches: 296, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 296 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (150 bp):
AGGTCATGTATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTATTCGTACCTGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGACT
ACTACGTGTATCAGATGGTT
Found at i:10655658 original size:16 final size:15
Alignment explanation
Indices: 10655620--10655658 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
10655610 TGGATTCTCA
*
10655620 TATCATGGATTTCTT
1 TATCTTGGATTTCTT
10655635 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
10655650 TATTCTTGG
1 TA-TCTTGG
10655659 CTTCTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:10661665 original size:31 final size:31
Alignment explanation
Indices: 10661627--10661700 Score: 123
Period size: 30 Copynumber: 2.4 Consensus size: 31
10661617 ACGGTTACTA
10661627 GGCCGAAGCCTTTTCAAAAATCAAATCACTG
1 GGCCGAAGCCTTTTCAAAAATCAAATCACTG
* *
10661658 GGCCGAAG-CTTTTCATAAATCATATCACTG
1 GGCCGAAGCCTTTTCAAAAATCAAATCACTG
10661688 GGCCGAAGCCTTT
1 GGCCGAAGCCTTT
10661701 ATTGTAAACG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 28 0.70
31 12 0.30
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (31 bp):
GGCCGAAGCCTTTTCAAAAATCAAATCACTG
Found at i:10661784 original size:42 final size:42
Alignment explanation
Indices: 10661724--10661815 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
10661714 TGGCCCATAG
*
10661724 GCCCATTTCAATAACACATGAAATATCAATGAATGTATACAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATACAA
* *
10661766 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATACAA
10661808 GCCCATTT
1 GCCCATTT
10661816 GGGGAGACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (42 bp):
GCCCATTTCAATAACACATGAAATACCAATGAATGTATACAA
Found at i:10661988 original size:25 final size:26
Alignment explanation
Indices: 10661960--10662108 Score: 221
Period size: 26 Copynumber: 5.8 Consensus size: 26
10661950 CCTCTTTAAT
*
10661960 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
**
10661985 AACTGGGGCA-AAGCCCTTTTTAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* * *
10662010 AATTGGGGCATAAGCCTTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGATA
10662036 AACTGGGGCATAAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
10662062 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
10662088 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
10662109 GCACTTCCTC
Statistics
Matches: 111, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
25 31 0.28
26 80 0.72
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGATA
Found at i:10662189 original size:11 final size:11
Alignment explanation
Indices: 10662158--10662213 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
10662148 TTATGAATTC
10662158 ATCATGTGCAT
1 ATCATGTGCAT
* *
10662169 TTCA--TACAT
1 ATCATGTGCAT
10662178 ATCATGTGCAT
1 ATCATGTGCAT
*
10662189 ATCA--TACAT
1 ATCATGTGCAT
10662198 ATCATGTGCAT
1 ATCATGTGCAT
10662209 ATCAT
1 ATCAT
10662214 ATAATTCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:10662223 original size:40 final size:38
Alignment explanation
Indices: 10662158--10662233 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 38
10662148 TTATGAATTC
* *
10662158 ATCATGTGCATTTCATACATATCATGTGCATATCATACAT
1 ATCATGTGCATATCATAAATATCATGT--ATATCATACAT
10662198 ATCATGTGCATATCATATAAT-TCATGTATATCATAC
1 ATCATGTGCATATCATA-AATATCATGTATATCATAC
10662234 CCCACGTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 9 0.27
40 22 0.67
41 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (38 bp):
ATCATGTGCATATCATAAATATCATGTATATCATACAT
Found at i:10662224 original size:20 final size:20
Alignment explanation
Indices: 10662158--10662214 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
10662148 TTATGAATTC
*
10662158 ATCATGTGCATTTCATACAT
1 ATCATGTGCATATCATACAT
10662178 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10662198 ATCATGTGCATATCATA
1 ATCATGTGCATATCATA
10662215 TAATTCATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10662957 original size:27 final size:28
Alignment explanation
Indices: 10662915--10662992 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
10662905 CACGGAACAT
10662915 AAGGGCATATT-C-GTCATTTTACCATAC
1 AAGGGC-TATTACGGTCATTTTACCATAC
* *
10662942 AAGGG-TATTACGGTCACTTTACCCTAC
1 AAGGGCTATTACGGTCATTTTACCATAC
* * *
10662969 AGGGGCTTTTACGGTCTTTTTACC
1 AAGGGCTATTACGGTCATTTTACC
10662993 TATTAGGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
25 4 0.10
26 1 0.02
27 22 0.52
28 15 0.36
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (28 bp):
AAGGGCTATTACGGTCATTTTACCATAC
Found at i:10663327 original size:80 final size:81
Alignment explanation
Indices: 10663133--10663340 Score: 231
Period size: 80 Copynumber: 2.6 Consensus size: 81
10663123 TTTGTAAATC
*** ** * * * *
10663133 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTATAGACCAGTGGTATTTT
*
10663198 GGTAACTTTACAAACT
66 GGTAACTTTACAAACG
* *
10663214 AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGCAATTTTATAGACCAG-GGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTATAGACCAGTGGTATTTT
* * *
10663278 GGTAATTTTACTGATCG
66 GGTAACTTTAC-AAACG
** *
10663295 A-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTT
10663341 GTAAATCGAG
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
80 58 0.54
81 50 0.46
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTATAGACCAGTGGTATTTT
GGTAACTTTACAAACG
Found at i:10663341 original size:27 final size:27
Alignment explanation
Indices: 10663023--10663345 Score: 217
Period size: 27 Copynumber: 12.0 Consensus size: 27
10663013 TTTCATCCTA
* * * *
10663023 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
**
10663050 CAAGGGTATTTCAGTAA-TTTAGTAAAC
1 CAAGGGTATTTTGGTAATTTTA-TAAAC
* * * * *
10663077 TAATGGTATTTCT-ATAATTTTTAGAAAGT
1 CAAGGGTATTT-TGGTAA-TTTTATAAA-C
* *
10663106 CAAGGGTATTTT-GTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * *
10663132 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAC
** * * *
10663159 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
10663186 C-AGTGGTATTTTGGTAACTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTATAAAC
* * *
10663213 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* * * * *
10663240 TAGGGGTATTTTAGCAATTTTATAGAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
10663267 C-AGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTGGTAATTTTA-TAAAC
* *
10663293 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAC
* *
10663320 CAAGGGTATTTTAGTAATTTTGTAAA
1 CAAGGGTATTTTGGTAATTTTATAAA
10663346 TCGAGGCTAA
Statistics
Matches: 239, Mismatches: 46, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
26 38 0.16
27 180 0.75
28 8 0.03
29 13 0.05
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAC
Found at i:10663364 original size:27 final size:27
Alignment explanation
Indices: 10663333--10663568 Score: 292
Period size: 27 Copynumber: 8.7 Consensus size: 27
10663323 GGGTATTTTA
* * **
10663333 GTAATTTTGTAAATCGAGGCTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* ** * *
10663360 ATAATTCTACAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
10663387 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
10663414 ATAATTCTATAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
10663441 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
10663468 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
10663495 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
10663522 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
**
10663549 GTAATTCTACAAATCGAGGG
1 GTAATTCTGTAAATCGAGGG
10663569 CATTTTAGTA
Statistics
Matches: 182, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 182 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:10663398 original size:81 final size:81
Alignment explanation
Indices: 10663304--10663581 Score: 299
Period size: 81 Copynumber: 3.4 Consensus size: 81
10663294 GAGGGTATTT
* * * * * * * * * *
10663304 TGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGCTAAAATAATAATTCTA
1 TGGTAATTCTGTAAATCGAGGGTATTATAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTA
* *
10663369 CAAATCAAGGGTAAAA
66 TAAATCGAGGGTAAAA
*
10663385 TGGTAATTCTGTAAATCGAGGGTA--AAACGATAATTCTATAAATCAAGGGTAAAACAGTAATTC
1 TGGTAATTCTGTAAATCGAGGGTATTATA-G-TAATTCTATAAATCAAGGGTAAAACAGTAATTC
*
10663448 TGTAAATCGAGGGTAAAA
64 TATAAATCGAGGGTAAAA
* * ** ** *
10663466 CGGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAACGGTAATTCTA
1 TGGTAATTCTGTAAATCGAGGGTATTATAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTA
10663531 TAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
** * *
10663547 TGGTAATTCTACAAATCGAGGGCATTTTAGTAATT
1 TGGTAATTCTGTAAATCGAGGGTATTATAGTAATT
10663582 TGGTAAACTA
Statistics
Matches: 163, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
79 1 0.01
80 1 0.01
81 159 0.98
82 1 0.01
83 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (81 bp):
TGGTAATTCTGTAAATCGAGGGTATTATAGTAATTCTATAAATCAAGGGTAAAACAGTAATTCTA
TAAATCGAGGGTAAAA
Found at i:10667261 original size:26 final size:26
Alignment explanation
Indices: 10667232--10667339 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
10667222 TGGTAAAAAT
10667232 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
10667258 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
10667284 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
10667310 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
10667336 TGAT
1 TGAT
10667340 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:10673723 original size:26 final size:26
Alignment explanation
Indices: 10673694--10673801 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
10673684 TGGTACAAAT
10673694 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
10673720 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
10673746 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
10673772 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
10673798 TGAT
1 TGAT
10673802 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:10677834 original size:13 final size:13
Alignment explanation
Indices: 10677816--10677840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10677806 GGATTTTTTA
10677816 TTAAACTAATTAT
1 TTAAACTAATTAT
10677829 TTAAACTAATTA
1 TTAAACTAATTA
10677841 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:10679185 original size:20 final size:19
Alignment explanation
Indices: 10679162--10679203 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
10679152 TAAAGAAAGT
10679162 AAAT-AAAATGGAAAGTAATG
1 AAATGAAAAT-GAAAGTAA-G
*
10679182 AAATGCAAATGAAAGTAAG
1 AAATGAAAATGAAAGTAAG
10679201 AAA
1 AAA
10679204 ATTTGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (19 bp):
AAATGAAAATGAAAGTAAG
Found at i:10679655 original size:15 final size:16
Alignment explanation
Indices: 10679635--10679665 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10679625 TTGGTGCCTT
10679635 TTTGAT-ATGTGTTAA
1 TTTGATAATGTGTTAA
10679650 TTTGATAATGTGTTAA
1 TTTGATAATGTGTTAA
10679666 AGCATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTGATAATGTGTTAA
Found at i:10694292 original size:77 final size:77
Alignment explanation
Indices: 10694165--10694307 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 77
10694155 AAGTACTTAT
* * * *
10694165 ATCATGGCCCGAAGCCAAATCAAGGTAACTTATATCCAAAGTACTGATATCATGGCCCGAAGCCA
1 ATCATGGCCCGAAGCCAAATCAAGATAACTCATACCCAAAGTACTAATATCATGGCCCGAAGCCA
10694230 AATTAGTCGATA
66 AATTAGTCGATA
* * * *
10694242 ATCATGGCCCGAAGCCAAATC-AGTATAACTCGTACCCGAAGTGCTAATATCATGGCCTGAAGCC
1 ATCATGGCCCGAAGCCAAATCAAG-ATAACTCATACCCAAAGTACTAATATCATGGCCCGAAGCC
10694306 AA
65 AA
10694308 CTCAATGTCT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 2 0.04
77 55 0.96
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (77 bp):
ATCATGGCCCGAAGCCAAATCAAGATAACTCATACCCAAAGTACTAATATCATGGCCCGAAGCCA
AATTAGTCGATA
Found at i:10696784 original size:27 final size:27
Alignment explanation
Indices: 10696754--10696807 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
10696744 TTTTTAAAGG
10696754 TTAAAATGGTAAATGAACAATAAAAAA
1 TTAAAATGGTAAATGAACAATAAAAAA
*
10696781 TTAAAATTGTAAATGAACAATAAAAAA
1 TTAAAATGGTAAATGAACAATAAAAAA
10696808 AATTAAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (27 bp):
TTAAAATGGTAAATGAACAATAAAAAA
Found at i:10701974 original size:6 final size:6
Alignment explanation
Indices: 10701958--10701999 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
10701948 TGGTTTTATC
*
10701958 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
10702000 GGAAATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:10701981 original size:18 final size:18
Alignment explanation
Indices: 10701958--10702007 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
10701948 TGGTTTTATC
10701958 AAAATGGAAATGAAAATG
1 AAAATGGAAATGAAAATG
*
10701976 AAAATGAAAATGAAAATG
1 AAAATGGAAATGAAAATG
10701994 AAAATGGGAAATGA
1 AAAAT-GGAAATGA
10702008 TTCATTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (18 bp):
AAAATGGAAATGAAAATG
Found at i:10705435 original size:43 final size:42
Alignment explanation
Indices: 10705369--10705529 Score: 132
Period size: 43 Copynumber: 3.8 Consensus size: 42
10705359 AGCTTGTACC
* * * *
10705369 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATTG
1 ATGCCAATGTCCCAAACGTGGTCTTACACGAAATCAAATA-CG
*
10705412 ATGCCACTGTCCCAAACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAAAC-GTGGTCTTACACGAAATCAAATACG
* * *
10705454 ATGCCAATGT-CCTAGCGATGGTCTTGCACGTAAATCATAACT-CG
1 ATGCCAATGTCCCAAACG-TGGTCTTACACG-AAATCA-AA-TACG
* * * *
10705498 ATGCCAACGT-CCAAATGTGCTCTTACATGAAA
1 ATGCCAATGTCCCAAACGTGGTCTTACACGAAA
10705530 ACACATATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
40 1 0.01
41 4 0.04
42 23 0.24
43 49 0.51
44 18 0.19
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAAACGTGGTCTTACACGAAATCAAATACG
Found at i:10706644 original size:13 final size:13
Alignment explanation
Indices: 10706625--10706662 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
10706615 CACAAACGAT
10706625 AAAATTTTCACAC
1 AAAATTTTCACAC
*
10706638 GAAATTTTCACAC
1 AAAATTTTCACAC
*
10706651 AAAACTTTCACA
1 AAAATTTTCACA
10706663 GATATCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.29
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:10713170 original size:44 final size:41
Alignment explanation
Indices: 10713088--10713182 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 41
10713078 TCCTAGATAG
*
10713088 GGTCTTACACGAAATCAAATACGATGCAATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATACGATGCAATGTCACAGACAT
*
10713129 GGTCTTACATGTAAATCATAACT-CGATGCCAATGTCACAGACAT
1 GGTCTTACACG-AAATCA-AA-TACGATG-CAATGTCACAGACAT
10713173 GGTCTTACAC
1 GGTCTTACAC
10713183 AAAAACACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
41 10 0.21
42 6 0.13
43 7 0.15
44 24 0.51
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
GGTCTTACACGAAATCAAATACGATGCAATGTCACAGACAT
Found at i:10715726 original size:30 final size:30
Alignment explanation
Indices: 10715690--10715753 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
10715680 TACCAGTAAC
* *
10715690 TACTTAGACTCTAGAGTGCATGCTAATTAT
1 TACTTAGAATCTAGAGTGCACGCTAATTAT
10715720 TACTTAGAATCTAGAGTGCACGCTAATTAT
1 TACTTAGAATCTAGAGTGCACGCTAATTAT
10715750 TACT
1 TACT
10715754 CAATTGCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (30 bp):
TACTTAGAATCTAGAGTGCACGCTAATTAT
Found at i:10718786 original size:19 final size:19
Alignment explanation
Indices: 10718762--10718806 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
10718752 ATGATATACC
*
10718762 ACATTTAACCATCACATGA
1 ACATTTAACCATAACATGA
* *
10718781 ACATTTAAGCATAACATGC
1 ACATTTAACCATAACATGA
10718800 ACATTTA
1 ACATTTA
10718807 GTAGGTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (19 bp):
ACATTTAACCATAACATGA
Found at i:10719801 original size:15 final size:16
Alignment explanation
Indices: 10719776--10719810 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
10719766 TTAAGAGTCT
10719776 ACTTCGAGTTACACGA
1 ACTTCGAGTTACACGA
10719792 ACTT-GAGTTACACGA
1 ACTTCGAGTTACACGA
10719807 ACTT
1 ACTT
10719811 ACCTGGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (16 bp):
ACTTCGAGTTACACGA
Found at i:10724493 original size:20 final size:20
Alignment explanation
Indices: 10724468--10724511 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
10724458 CATAGGAGGG
*
10724468 CAAAAAGAGCGAGAAACGGGC
1 CAAAAAGAGAGA-AAACGGGC
*
10724489 CAAAAATAGAGAAAACGGGC
1 CAAAAAGAGAGAAAACGGGC
10724509 CAA
1 CAA
10724512 CGTGGGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.52, C:0.18, G:0.27, T:0.02
Consensus pattern (20 bp):
CAAAAAGAGAGAAAACGGGC
Found at i:10742812 original size:27 final size:27
Alignment explanation
Indices: 10742782--10742959 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
10742772 ATATTGAGTC
* * * *
10742782 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
10742809 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10742836 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
10742864 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
10742891 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
10742918 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
10742945 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10742960 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:10742921 original size:82 final size:81
Alignment explanation
Indices: 10742803--10742958 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
10742793 TGCTATATAA
* *
10742803 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
10742868 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
10742885 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
10742949 CACTTAGTGC
65 CACTTAGTGC
10742959 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:10746326 original size:27 final size:27
Alignment explanation
Indices: 10746296--10746473 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
10746286 ATATTGAGTC
* *
10746296 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
10746323 CGCACACTTAGTGCTACGTAATCCAA-T
1 CGCACACTTAGTGCTACATAAT-CAACT
*
10746350 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
10746378 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
10746405 TGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
10746432 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
10746459 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10746474 GTACAATTTA
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 101 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:10750176 original size:34 final size:34
Alignment explanation
Indices: 10750099--10750224 Score: 110
Period size: 34 Copynumber: 3.7 Consensus size: 34
10750089 TTCAGTTAGG
* * * * * *
10750099 GCCTTAGCCTATTTCAGCAACAGTACCAGT-GGG
1 GCCTTAGCCCATTTCAGTAACAGTAGCAATCTGA
* * *
10750132 GCCTAAGCCCATATCAGTAACAGTGGCAATCTGA
1 GCCTTAGCCCATTTCAGTAACAGTAGCAATCTGA
* * *
10750166 GCCTTAGCCCATTTCAATAACAGTAGTAATCTGG
1 GCCTTAGCCCATTTCAGTAACAGTAGCAATCTGA
** *
10750200 GTTTTAGCCCATTTTAGTAACAGTA
1 GCCTTAGCCCATTTCAGTAACAGTA
10750225 ATCAGTGCAG
Statistics
Matches: 73, Mismatches: 19, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
33 23 0.32
34 50 0.68
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (34 bp):
GCCTTAGCCCATTTCAGTAACAGTAGCAATCTGA
Found at i:10750238 original size:18 final size:18
Alignment explanation
Indices: 10750215--10750271 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
10750205 AGCCCATTTT
10750215 AGTAACAGTAATCAGTGC
1 AGTAACAGTAATCAGTGC
*
10750233 AGTAACCA-TAATCAATGC
1 AGTAA-CAGTAATCAGTGC
10750251 AGTAACAGTAATCAGTGC
1 AGTAACAGTAATCAGTGC
10750269 AGT
1 AGT
10750272 GTACAAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 2 0.06
18 31 0.89
19 2 0.06
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (18 bp):
AGTAACAGTAATCAGTGC
Found at i:10757209 original size:22 final size:23
Alignment explanation
Indices: 10757184--10757242 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
10757174 CAACCAAATC
10757184 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
10757206 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
10757229 ACA-TCATCACATAT
1 A-ATTCAT-ACATAT
10757243 CTAAAACCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 18 0.58
24 7 0.23
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:10757901 original size:54 final size:54
Alignment explanation
Indices: 10757819--10757951 Score: 266
Period size: 54 Copynumber: 2.5 Consensus size: 54
10757809 CCTTGCAATG
10757819 GGATTACCAGTCCAGGCTAAATCCCATATAATATAAACTCATAGAGTATTGTCA
1 GGATTACCAGTCCAGGCTAAATCCCATATAATATAAACTCATAGAGTATTGTCA
10757873 GGATTACCAGTCCAGGCTAAATCCCATATAATATAAACTCATAGAGTATTGTCA
1 GGATTACCAGTCCAGGCTAAATCCCATATAATATAAACTCATAGAGTATTGTCA
10757927 GGATTACCAGTCCAGGCTAAATCCC
1 GGATTACCAGTCCAGGCTAAATCCC
10757952 CTGCAACGAC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (54 bp):
GGATTACCAGTCCAGGCTAAATCCCATATAATATAAACTCATAGAGTATTGTCA
Found at i:10760067 original size:42 final size:43
Alignment explanation
Indices: 10760021--10760114 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
10760011 TCCTAGATAG
*
10760021 GGTCTTACACAAAATCACAATA-GATGCCAATGTCCCAAACAT
1 GGTCTTACACAAAATCACAATACAATGCCAATGTCCCAAACAT
** * * *
10760063 GGTCTTACACGTAATCTCAATACAATGCCAATGTCCTAGACAT
1 GGTCTTACACAAAATCACAATACAATGCCAATGTCCCAAACAT
10760106 GGTCTTACA
1 GGTCTTACA
10760115 TGTTATCGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
42 19 0.42
43 26 0.58
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (43 bp):
GGTCTTACACAAAATCACAATACAATGCCAATGTCCCAAACAT
Found at i:10760106 original size:43 final size:42
Alignment explanation
Indices: 10760002--10760114 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
10759992 ATACATATCG
* * * * *
10760002 ATGCCACTATCCTAGATAGGGTCTTACACAAAATCACAATAG
1 ATGCCAATGTCCTAGACATGGTCTTACACAAAATCACAATAA
* * ** *
10760044 ATGCCAATGTCCCAAACATGGTCTTACACGTAATCTCAATACA
1 ATGCCAATGTCCTAGACATGGTCTTACACAAAATCACAATA-A
10760087 ATGCCAATGTCCTAGACATGGTCTTACA
1 ATGCCAATGTCCTAGACATGGTCTTACA
10760115 TGTTATCGCA
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 32 0.55
43 26 0.45
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCTAGACATGGTCTTACACAAAATCACAATAA
Found at i:10764349 original size:48 final size:48
Alignment explanation
Indices: 10764275--10764450 Score: 257
Period size: 48 Copynumber: 3.7 Consensus size: 48
10764265 CATTAGGGGA
* *
10764275 TTCATTTATTTGGCTTCAGGCCATGATATTGGCACTTCAGGTGCGAGC
1 TTCATTGATTTGGCTTCAGGCCATGATATTGGCACTTCGGGTGCGAGC
*
10764323 TTCATTGATTTGGCTTCAGGCTATGATATTGGCACTTCGGGTGCGAGC
1 TTCATTGATTTGGCTTCAGGCCATGATATTGGCACTTCGGGTGCGAGC
* *
10764371 TTCATTGATTTGGCTTCAGGCCATGATATTAGCACTTTGGGTGCGAG-
1 TTCATTGATTTGGCTTCAGGCCATGATATTGGCACTTCGGGTGCGAGC
* * **
10764418 AT-ATTGAGTTGGCTTTGGGCCATGATATTGGCA
1 TTCATTGATTTGGCTTCAGGCCATGATATTGGCA
10764451 TTTAGTCTAC
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
46 27 0.23
47 1 0.01
48 89 0.76
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.36
Consensus pattern (48 bp):
TTCATTGATTTGGCTTCAGGCCATGATATTGGCACTTCGGGTGCGAGC
Found at i:10776541 original size:12 final size:12
Alignment explanation
Indices: 10776524--10776553 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
10776514 TTTCAAATGG
10776524 CCAAAATCATTA
1 CCAAAATCATTA
10776536 CCAAAATCATTA
1 CCAAAATCATTA
10776548 CCAAAA
1 CCAAAA
10776554 CATAACTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (12 bp):
CCAAAATCATTA
Found at i:10778848 original size:12 final size:12
Alignment explanation
Indices: 10778831--10778860 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
10778821 TTTCAAATGG
10778831 CCAAAATCATTA
1 CCAAAATCATTA
10778843 CCAAAATCATTA
1 CCAAAATCATTA
10778855 CCAAAA
1 CCAAAA
10778861 CATAACTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (12 bp):
CCAAAATCATTA
Found at i:10788159 original size:15 final size:15
Alignment explanation
Indices: 10788139--10788184 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
10788129 CATGTTGTTA
10788139 TATTATATTAACCTT
1 TATTATATTAACCTT
10788154 TATTATATTAA--TT
1 TATTATATTAACCTT
*
10788167 TACTA-ATTTAACCTT
1 TATTATA-TTAACCTT
10788182 TAT
1 TAT
10788185 AATAATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.38
15 15 0.58
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATATTAACCTT
Found at i:10790184 original size:43 final size:43
Alignment explanation
Indices: 10790047--10790219 Score: 176
Period size: 43 Copynumber: 4.0 Consensus size: 43
10790037 ACATAGGATT
* *
10790047 TCGATATGTG-TTATCGTGTAAGACCACGTCTAGGACGTTGGCA
1 TCGATATTTGATT-TCGTGTAAGACCACGTCTGGGACGTTGGCA
* ** * *
10790090 TCAAT-TTGTGATTTACGTGTTTGACCATGTCTGGGACATTGGCA
1 TCGATATT-TGATTT-CGTGTAAGACCACGTCTGGGACGTTGGCA
**
10790134 TCG-TATTTGATTTCGTGTAAGACCTTGTCTGGGACAG-TGGCA
1 TCGATATTTGATTTCGTGTAAGACCACGTCTGGGAC-GTTGGCA
*
10790176 TCGATATTTGATTACAG-GTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATTTGATTTC-GTGTAAGACCACGTCTGGGACGTTGGCA
10790219 T
1 T
10790220 TGTACGAGCT
Statistics
Matches: 107, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
42 29 0.27
43 47 0.44
44 31 0.29
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (43 bp):
TCGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:10794895 original size:40 final size:39
Alignment explanation
Indices: 10794840--10794917 Score: 138
Period size: 40 Copynumber: 2.0 Consensus size: 39
10794830 NNNNNNNTGC
*
10794840 TGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGT
1 TGGTGATGTATCCGGGCTAAGCCCCGAAG-GCATTCGTGT
10794880 TGGTGATGTATCCGGGCTAAGCCCCGAAGGCATTCGTG
1 TGGTGATGTATCCGGGCTAAGCCCCGAAGGCATTCGTG
10794918 CTGGGACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (39 bp):
TGGTGATGTATCCGGGCTAAGCCCCGAAGGCATTCGTGT
Found at i:10794932 original size:39 final size:40
Alignment explanation
Indices: 10794849--10794933 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
10794839 CTGGTGATGT
* * ***
10794849 ATCCGGGCTAAGTCCCGAAGAGCATTCGTGTTGGTGATGT
1 ATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTGGTGAAAA
10794889 ATCCGGGCTAAGCCCCGAAG-GCATTCGTGCTGG-GACAAA
1 ATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTGGTGA-AAA
10794928 ATCCGG
1 ATCCGG
10794934 ACTTGAGGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 2 0.05
39 18 0.46
40 19 0.49
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.21
Consensus pattern (40 bp):
ATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTGGTGAAAA
Found at i:10795212 original size:25 final size:24
Alignment explanation
Indices: 10795166--10795215 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
10795156 TGTGTAATAA
*
10795166 CGAATGAATAGGGCATTATGTGTG
1 CGAATGAATAGGGCACTATGTGTG
* *
10795190 CGAATGATTAGAGGCACTGTGTGTG
1 CGAATGAATAG-GGCACTATGTGTG
10795215 C
1 C
10795216 AAATTCCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.26, C:0.12, G:0.34, T:0.28
Consensus pattern (24 bp):
CGAATGAATAGGGCACTATGTGTG
Found at i:10795236 original size:29 final size:29
Alignment explanation
Indices: 10795203--10795362 Score: 94
Period size: 29 Copynumber: 5.5 Consensus size: 29
10795193 ATGATTAGAG
*
10795203 GCACTGTGTGTGCAAATTCCTTTAACCGA
1 GCACTATGTGTGCAAATTCCTTTAACCGA
* ** **
10795232 GCACTATGTGTGCGAGA-T-CGGTAATTGA
1 GCACTATGTGTGC-AAATTCCTTTAACCGA
* * *
10795260 GGCACTGTGTGTGCGAATTCCTTCAACCGA
1 -GCACTATGTGTGCAAATTCCTTTAACCGA
* * * ** **
10795290 GCATTATGTGTTCGAGATT--GGTAATTGA
1 GCACTATGTGTGC-AAATTCCTTTAACCGA
* *
10795318 GGCACTGTGTGTGCGAATTCCTTTAACCGA
1 -GCACTATGTGTGCAAATTCCTTTAACCGA
10795348 GCACTATGTGTGCAA
1 GCACTATGTGTGCAA
10795363 GACCGGTAAT
Statistics
Matches: 88, Mismatches: 35, Indels: 16
0.63 0.25 0.12
Matches are distributed among these distances:
28 14 0.16
29 59 0.67
30 15 0.17
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (29 bp):
GCACTATGTGTGCAAATTCCTTTAACCGA
Found at i:10795380 original size:29 final size:29
Alignment explanation
Indices: 10795232--10795389 Score: 79
Period size: 29 Copynumber: 5.4 Consensus size: 29
10795222 CTTTAACCGA
* *
10795232 GCACTATGTGTGCGAGATCGGTAATTGAG
1 GCACTATGTGTGCAAGACCGGTAATTGAG
* ** * **
10795261 GCACTGTGTGTGCGAATTCC-TTCAACCGA-
1 GCACTATGTGTGC-AAGACCGGT-AATTGAG
* * * **
10795290 GCATTATGTGTTCGAGATTGGTAATTGAG
1 GCACTATGTGTGCAAGACCGGTAATTGAG
* ** ** **
10795319 GCACTGTGTGTGCGAATTCCTTTAACCGA-
1 GCACTATGTGTGC-AAGACCGGTAATTGAG
10795348 GCACTATGTGTGCAAGACCGGTAATTGAG
1 GCACTATGTGTGCAAGACCGGTAATTGAG
*
10795377 GCACTGTGTGTGC
1 GCACTATGTGTGC
10795390 GAGTTCTTCA
Statistics
Matches: 84, Mismatches: 39, Indels: 12
0.62 0.29 0.09
Matches are distributed among these distances:
28 14 0.17
29 58 0.69
30 12 0.14
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (29 bp):
GCACTATGTGTGCAAGACCGGTAATTGAG
Found at i:10795446 original size:58 final size:58
Alignment explanation
Indices: 10795200--10795426 Score: 366
Period size: 58 Copynumber: 3.9 Consensus size: 58
10795190 CGAATGATTA
* *
10795200 GAGGCACTGTGTGTGCAAATTCCTTTAACCGAGCACTATGTGTGCGAGATCGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
* * *
10795258 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCATTATGTGTTCGAGATTGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
* * *
10795316 GAGGCACTGTGTGTGCGAATTCCTTTAACCGAGCACTATGTGTGCAAGACCGGTAATT
1 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
*
10795374 GAGGCACTGTGTGTGCGAGTT-CTTCAACCGAGCACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGT
10795427 CAGTGGGCAC
Statistics
Matches: 154, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
57 29 0.19
58 125 0.81
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (58 bp):
GAGGCACTGTGTGTGCGAATTCCTTCAACCGAGCACTATGTGTGCGAGATCGGTAATT
Found at i:10799148 original size:78 final size:78
Alignment explanation
Indices: 10799007--10799163 Score: 194
Period size: 78 Copynumber: 2.0 Consensus size: 78
10798997 ATTTGATGTG
10799007 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTT
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTT
10799072 CGTGCTGGTATTA
66 CGTGCTGGTATTA
* * * * * * *
10799085 TATCCGGG-TTAAA-TCCCGCAGGCCTA-GTGCTGGTATTATATCTGAGTTTAAAGTCCCGTAGG
1 TATCCGGGCTTAAAGACCCGCAGG-CTATATGCTAGAATTATATCCG-GGTTAAA-TCCCGCAGG
*
10799147 CTTCGTGCTGGTGTTA
63 CTTCGTGCTGGTATTA
10799163 T
1 T
10799164 GTTTGGGTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
76 22 0.32
77 14 0.21
78 32 0.47
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (78 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTATATCCGGGTTAAATCCCGCAGGCTT
CGTGCTGGTATTA
Found at i:10799155 original size:40 final size:38
Alignment explanation
Indices: 10799007--10799163 Score: 172
Period size: 38 Copynumber: 4.0 Consensus size: 38
10798997 ATTTGATGTG
* * * *
10799007 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTAGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGTATTA
10799047 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* *
10799085 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* * * *
10799123 TATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGGTGTTA
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
10799163 T
1 T
10799164 GTTTGGGTTT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.01
38 60 0.59
39 11 0.11
40 30 0.29
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
Found at i:10801913 original size:43 final size:43
Alignment explanation
Indices: 10801847--10801928 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
10801837 TTTCTCAGTC
10801847 ATCAAATATTTCAAACTTTTATGATCAGAATAAACATGAAATT
1 ATCAAATATTTCAAACTTTTATGATCAGAATAAACATGAAATT
*
10801890 ATCAGATATTTCAAACTTTTATGATCAGAATAAACATGA
1 ATCAAATATTTCAAACTTTTATGATCAGAATAAACATGA
10801929 CATTTCTCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (43 bp):
ATCAAATATTTCAAACTTTTATGATCAGAATAAACATGAAATT
Found at i:10801916 original size:23 final size:23
Alignment explanation
Indices: 10801847--10801918 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
10801837 TTTCTCAGTC
*
10801847 ATCAAATATTTCAAACTTTTATG
1 ATCAGATATTTCAAACTTTTATG
*** *
10801870 ATCAGA-A--T-AAACATGAAATT
1 ATCAGATATTTCAAAC-TTTTATG
10801890 ATCAGATATTTCAAACTTTTATG
1 ATCAGATATTTCAAACTTTTATG
10801913 ATCAGA
1 ATCAGA
10801919 ATAAACATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
19 4 0.11
20 10 0.29
21 1 0.03
22 1 0.03
23 15 0.43
24 4 0.11
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (23 bp):
ATCAGATATTTCAAACTTTTATG
Found at i:10806442 original size:42 final size:43
Alignment explanation
Indices: 10806334--10806446 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
10806324 AACTCGTACA
10806334 ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATCG
* * * *
10806377 ACGCCACTGTCCCAGACAG-GGTCTTACAT-TAAATCTCAA-AT-G
1 ATGCCAATGTCCCAGA-TGTGGTCTTACATGT-AATC-AAATATCG
10806419 ATGCCAATGTCCCAGATGTGGTCTTACA
1 ATGCCAATGTCCCAGATGTGGTCTTACA
10806447 CGAAAACACA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 25 0.42
43 30 0.51
44 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATCG
Found at i:10810398 original size:16 final size:16
Alignment explanation
Indices: 10810365--10810398 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10810355 ATACGCTATT
* *
10810365 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
10810381 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
10810397 AA
1 AA
10810399 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:10813225 original size:21 final size:21
Alignment explanation
Indices: 10813199--10813239 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10813189 AGACGAGCAA
* *
10813199 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
10813220 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
10813240 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:10815178 original size:16 final size:16
Alignment explanation
Indices: 10815145--10815178 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10815135 GGAGATTGTT
* *
10815145 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
10815161 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
10815177 AA
1 AA
10815179 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:10823246 original size:7 final size:7
Alignment explanation
Indices: 10823234--10823266 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
10823224 CATTTTTAAT
10823234 TATTTTA
1 TATTTTA
10823241 TATTTTA
1 TATTTTA
*
10823248 TAATTTA
1 TATTTTA
10823255 TATTTTA
1 TATTTTA
10823262 TATTT
1 TATTT
10823267 AAATTAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TATTTTA
Found at i:10826019 original size:20 final size:20
Alignment explanation
Indices: 10825994--10826033 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10825984 AACCAATTTT
10825994 CCCTAACTCAATTTAAGCAA
1 CCCTAACTCAATTTAAGCAA
10826014 CCCTAACTCAATTTAAGCAA
1 CCCTAACTCAATTTAAGCAA
10826034 AATGAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.25
Consensus pattern (20 bp):
CCCTAACTCAATTTAAGCAA
Found at i:10833330 original size:20 final size:18
Alignment explanation
Indices: 10833288--10833330 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
10833278 TTACTTGGCT
*
10833288 TTAAAAATACTGGAAATA
1 TTAAAAATACTGGAAAAA
*
10833306 TTAAAAATAAGTGGTAAAAA
1 TTAAAAAT-ACTGG-AAAAA
10833326 TTAAA
1 TTAAA
10833331 TTGAAGTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 4 0.19
20 9 0.43
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.28
Consensus pattern (18 bp):
TTAAAAATACTGGAAAAA
Found at i:10839494 original size:29 final size:29
Alignment explanation
Indices: 10839456--10839548 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
10839446 TTTATTGTCC
10839456 CTCTCTCTCATCTTCTTCATCTAATCTTTT
1 CTCT-TCTCATCTTCTTCATCTAATCTTTT
* **
10839486 CTCTTCTCATCTTCTTCATCATCACTCTTAA
1 CTCTTCTCATCTTCTTCATC-T-AATCTTTT
*
10839517 C-C-ACTCATCTTCTTCATCTAATCTTTT
1 CTCTTCTCATCTTCTTCATCTAATCTTTT
10839544 CTCTT
1 CTCTT
10839549 AACATGAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
27 6 0.12
28 2 0.04
29 31 0.61
30 6 0.12
31 6 0.12
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.49
Consensus pattern (29 bp):
CTCTTCTCATCTTCTTCATCTAATCTTTT
Found at i:10839990 original size:143 final size:145
Alignment explanation
Indices: 10839727--10840016 Score: 424
Period size: 143 Copynumber: 2.0 Consensus size: 145
10839717 TCCAAATCAC
* * * *
10839727 ATTTTATAGATCTATTATTAAAAAATGGGTTTTAGTTTTAGTTTTTCTGTTATCTTCTAGAAATT
1 ATTTTACAGATCTATTATTAAAAAACGAGTTTTAGTTTTAATTTTTCTGTTATCTTCTAGAAATT
** *
10839792 GATTGAGAGTTGAAACTATTGAGAAATAAATCTTTATTCTTTCTTGTTATATTCTAGAAATTGAT
66 GATCAAGAGTTGAAACTATTGAGAAATAAATCTTTATTCTTTCTTATTATATTCTAGAAATTGAT
10839857 GGAGAGTAGAAGAGA
131 GGAGAGTAGAAGAGA
* *
10839872 ATTTTACAGATCTATTATTAAGAAACGAGTTTTAGTTTTAATTTTT-T-TTATCTTCTGGAAATT
1 ATTTTACAGATCTATTATTAAAAAACGAGTTTTAGTTTTAATTTTTCTGTTATCTTCTAGAAATT
* * * * *
10839935 GGTCAAGAGTTGAAAGTGTTGAGAAA-AGAATTTTTATTCTTTCTTATTATGTTCTAGAAATTGA
66 GATCAAGAGTTGAAACTATTGAGAAATA-AATCTTTATTCTTTCTTATTATATTCTAGAAATTGA
10839999 TGGAGAGTAGAAGAGA
130 TGGAGAGTAGAAGAGA
10840015 AT
1 AT
10840017 GAGGAGTAAG
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
142 1 0.01
143 87 0.67
144 1 0.01
145 41 0.32
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (145 bp):
ATTTTACAGATCTATTATTAAAAAACGAGTTTTAGTTTTAATTTTTCTGTTATCTTCTAGAAATT
GATCAAGAGTTGAAACTATTGAGAAATAAATCTTTATTCTTTCTTATTATATTCTAGAAATTGAT
GGAGAGTAGAAGAGA
Found at i:10847010 original size:17 final size:17
Alignment explanation
Indices: 10846985--10847020 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
10846975 ACATGTACTC
10846985 ACATGCCATTAATTTAT
1 ACATGCCATTAATTTAT
*
10847002 ACATTCCATTAATTTAT
1 ACATGCCATTAATTTAT
10847019 AC
1 AC
10847021 GTTTCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (17 bp):
ACATGCCATTAATTTAT
Found at i:10848071 original size:17 final size:18
Alignment explanation
Indices: 10848037--10848071 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10848027 ACGGTGTTAA
*
10848037 ATAAAACATATTATAAAT
1 ATAAAACATATTAAAAAT
10848055 ATAAAACA-ATTAAAAAT
1 ATAAAACATATTAAAAAT
10848072 GAAGCAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAACATATTAAAAAT
Found at i:10849621 original size:95 final size:95
Alignment explanation
Indices: 10849459--10849709 Score: 333
Period size: 95 Copynumber: 2.7 Consensus size: 95
10849449 CATGGTGCTG
* * * * * * * * *
10849459 CTCACACAAGCTATGAAGAAT-CGTAGTACATCCAGAATCTTAGCCATTGGCAAGGTATCCACTA
1 CTCACACGAGCTATGAAGAATCCGCAATATATGCAGGATCTTAGCCATCGGTAAGGTATCCAATA
10849523 AATCGAAACATTAACCGTTACACAATACTA
66 AATCGAAACATTAACCGTTACACAATACTA
* * *
10849553 TTCACACGAGCTGTGAAGAATCCGCAATATATGCAGGATCTTAGCCATCGATAAGGTATCCAATA
1 CTCACACGAGCTATGAAGAATCCGCAATATATGCAGGATCTTAGCCATCGGTAAGGTATCCAATA
** * * *
10849618 AATCGCGACATTAACTGTTACACAATGCTG
66 AATCGAAACATTAACCGTTACACAATACTA
*
10849648 CTCACACGAGCTATGAAGAATCCGCAATATATGCAAGATCTTAGCCATCGGTAAGGTATCCA
1 CTCACACGAGCTATGAAGAATCCGCAATATATGCAGGATCTTAGCCATCGGTAAGGTATCCA
10849710 CCACTAGTAC
Statistics
Matches: 135, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
94 18 0.13
95 117 0.87
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (95 bp):
CTCACACGAGCTATGAAGAATCCGCAATATATGCAGGATCTTAGCCATCGGTAAGGTATCCAATA
AATCGAAACATTAACCGTTACACAATACTA
Found at i:10854446 original size:6 final size:6
Alignment explanation
Indices: 10854435--10854465 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
10854425 TAAATAAAGG
10854435 AAAATA AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA A
10854466 TAAAAGGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:10856624 original size:20 final size:20
Alignment explanation
Indices: 10856601--10856654 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
10856591 TGTGGTACCT
*
10856601 CACACGTCCGTGTGTCTGAA
1 CACACGACCGTGTGTCTGAA
*
10856621 CACACGACCATGTGTCTGAA
1 CACACGACCGTGTGTCTGAA
10856641 CACACGACCGTGTG
1 CACACGACCGTGTG
10856655 CCTTGCCTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (20 bp):
CACACGACCGTGTGTCTGAA
Found at i:10865663 original size:23 final size:23
Alignment explanation
Indices: 10865619--10865663 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
10865609 GAAAGAATAA
* *
10865619 ACCTTTGTGGAGAATTATGAAAG
1 ACCTTTGTGGAGAACTACGAAAG
*
10865642 ACCTTTGTGGTGAACTACGAAA
1 ACCTTTGTGGAGAACTACGAAA
10865664 AAATAAGCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (23 bp):
ACCTTTGTGGAGAACTACGAAAG
Found at i:10865712 original size:28 final size:28
Alignment explanation
Indices: 10865642--10865712 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
10865632 ATTATGAAAG
* *
10865642 ACCTTTGTGGTGAACTACGAAAAAATAA
1 ACCTTTGCGGTGAACTACAAAAAAATAA
* *
10865670 GCCTTTGCGATGAACTACAAAAAAATAA
1 ACCTTTGCGGTGAACTACAAAAAAATAA
*
10865698 ACCTTTGCGGCGAAC
1 ACCTTTGCGGTGAAC
10865713 AATAATGATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (28 bp):
ACCTTTGCGGTGAACTACAAAAAAATAA
Found at i:10866201 original size:47 final size:47
Alignment explanation
Indices: 10866132--10866276 Score: 263
Period size: 47 Copynumber: 3.1 Consensus size: 47
10866122 GGGTTAGTAG
10866132 AATCGGGTTTGTGAATCGAGAGAGAGTGGCCATGCCTTAATTTTTAA
1 AATCGGGTTTGTGAATCGAGAGAGAGTGGCCATGCCTTAATTTTTAA
*
10866179 AATCGGGTTTGTGAATCGAGAGAGAGTGGCCATGCCTTAATTTTTGA
1 AATCGGGTTTGTGAATCGAGAGAGAGTGGCCATGCCTTAATTTTTAA
*
10866226 AATCGGGTTTGTGAATCGAGAGAGAGTGGTCATGCCTTAATTTTTGAA
1 AATCGGGTTTGTGAATCGAGAGAGAGTGGCCATGCCTTAATTTTT-AA
10866274 AAT
1 AAT
10866277 TTATCTATGC
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 90 0.96
48 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (47 bp):
AATCGGGTTTGTGAATCGAGAGAGAGTGGCCATGCCTTAATTTTTAA
Found at i:10870585 original size:21 final size:21
Alignment explanation
Indices: 10870561--10870606 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10870551 AAGGGAGGAA
10870561 AAGGCCCAAACCATCCACTTG
1 AAGGCCCAAACCATCCACTTG
* *
10870582 AAGGCCCAAATCGTCCACTTG
1 AAGGCCCAAACCATCCACTTG
10870603 AAGG
1 AAGG
10870607 AAAAACTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.15
Consensus pattern (21 bp):
AAGGCCCAAACCATCCACTTG
Found at i:10872549 original size:15 final size:15
Alignment explanation
Indices: 10872524--10872560 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
10872514 TAATTAATCC
10872524 TAATTATATTAATTAA
1 TAATTA-ATTAATTAA
10872540 TAATTAATTAATTAA
1 TAATTAATTAATTAA
10872555 -AATTAA
1 TAATTAA
10872561 ACATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTAATTAATTAA
Found at i:10875819 original size:93 final size:93
Alignment explanation
Indices: 10875707--10875877 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
10875697 GCCCATAAGT
* *
10875707 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
10875772 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
10875800 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
10875865 CGAGTTCGGATGC
66 CGAGTTCGGATGC
10875878 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:10875874 original size:46 final size:46
Alignment explanation
Indices: 10875699--10875874 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
10875689 TGTAACCCGC
* * *
10875699 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10875745 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
10875795 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
10875838 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
10875875 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:10877964 original size:27 final size:26
Alignment explanation
Indices: 10877934--10878200 Score: 214
Period size: 27 Copynumber: 9.9 Consensus size: 26
10877924 AGACAGTTCA
* *
10877934 TTCAGATTTTACCACAAAGACTATTCC
1 TTCAGAGTTCACCACAAAGACTA-TCC
*
10877961 TTCAAAGTTCACCACAAAGACTATTCC
1 TTCAGAGTTCACCACAAAGACTA-TCC
* * *
10877988 TTCAAAGTTCGCCACAAAGAGTATTCC
1 TTCAGAGTTCACCACAAAGACTA-TCC
* * **
10878015 TTCAGAGTTCACCATAAGGGTTATCC
1 TTCAGAGTTCACCACAAAGACTATCC
* * * *
10878041 TTTTAGAGTTCGCCATAAAGGCTATCC
1 -TTCAGAGTTCACCACAAAGACTATCC
*
10878068 TTTCAGAGTT-AGCCACAAAGGCTATCC
1 -TTCAGAGTTCA-CCACAAAGACTATCC
* *
10878095 TTTCAGAGTTTACCACGAAGACTATCC
1 -TTCAGAGTTCACCACAAAGACTATCC
*
10878122 TTACAGAGTTCACCACAAAGTCTATCC
1 TT-CAGAGTTCACCACAAAGACTATCC
** * *
10878149 TTACAGAGTTTTCCACAAAGGCTACCC
1 TT-CAGAGTTCACCACAAAGACTATCC
*
10878176 TAAT-AGAGTTCACCACAAAGGCTAT
1 T--TCAGAGTTCACCACAAAGACTAT
10878201 GAAAATGCCA
Statistics
Matches: 204, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
26 5 0.02
27 197 0.97
28 1 0.00
29 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (26 bp):
TTCAGAGTTCACCACAAAGACTATCC
Found at i:10878004 original size:54 final size:53
Alignment explanation
Indices: 10877945--10878200 Score: 248
Period size: 54 Copynumber: 4.7 Consensus size: 53
10877935 TCAGATTTTA
* * *
10877945 CCACAAAGACTATTCCTTCAAAGTTCACCACAAAGACTATTCC-TTCAAAGTTCG
1 CCACAAAGACTA-TCCTTCAGAGTTCACCACAAAGGCTA-TCCTTTCAGAGTTCG
* * * * *
10877999 CCACAAAGAGTATTCCTTCAGAGTTCACCATAAGGGTTATCCTTTTAGAGTTCG
1 CCACAAAGACTA-TCCTTCAGAGTTCACCACAAAGGCTATCCTTTCAGAGTTCG
* * **
10878053 CCATAAAGGCTATCCTTTCAGAGTT-AGCCACAAAGGCTATCCTTTCAGAGTTTA
1 CCACAAAGACTATCC-TTCAGAGTTCA-CCACAAAGGCTATCCTTTCAGAGTTCG
* * * **
10878107 CCACGAAGACTATCCTTACAGAGTTCACCACAAAGTCTATCCTTACAGAGTTTT
1 CCACAAAGACTATCCTT-CAGAGTTCACCACAAAGGCTATCCTTTCAGAGTTCG
* *
10878161 CCACAAAGGCTACCCTAAT-AGAGTTCACCACAAAGGCTAT
1 CCACAAAGACTATCCT--TCAGAGTTCACCACAAAGGCTAT
10878201 GAAAATGCCA
Statistics
Matches: 168, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
53 9 0.05
54 157 0.93
55 1 0.01
56 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (53 bp):
CCACAAAGACTATCCTTCAGAGTTCACCACAAAGGCTATCCTTTCAGAGTTCG
Found at i:10880882 original size:15 final size:16
Alignment explanation
Indices: 10880862--10880894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10880852 TGGTTAAACT
10880862 AAGGAG-AGGGGAAGA
1 AAGGAGTAGGGGAAGA
*
10880877 AAGGAGTAGGTGAAGA
1 AAGGAGTAGGGGAAGA
10880893 AA
1 AA
10880895 ACTAGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.45, T:0.06
Consensus pattern (16 bp):
AAGGAGTAGGGGAAGA
Found at i:10880962 original size:14 final size:15
Alignment explanation
Indices: 10880943--10880971 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10880933 TATGACTGCA
10880943 ATGAGAAGAG-GGAG
1 ATGAGAAGAGTGGAG
10880957 ATGAGAAGAGTGGAG
1 ATGAGAAGAGTGGAG
10880972 GTACGATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.48, T:0.10
Consensus pattern (15 bp):
ATGAGAAGAGTGGAG
Found at i:10882595 original size:27 final size:27
Alignment explanation
Indices: 10882565--10882651 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
10882555 GCTAAAAAAT
*
10882565 GCCTTTGTGGCACACTCTGAATGAATA
1 GCCTTTGTGGCATACTCTGAATGAATA
*
10882592 GCC--TATGGCATACTCTGTATAT-ATATA
1 GCCTTTGTGGCATACTCTG-A-ATGA-ATA
* * *
10882619 GCCTTTGTGGCATACTCTGTATGGATC
1 GCCTTTGTGGCATACTCTGAATGAATA
10882646 GCCTTT
1 GCCTTT
10882652 ATGGTATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 12 0.25
26 2 0.04
27 21 0.44
29 13 0.27
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (27 bp):
GCCTTTGTGGCATACTCTGAATGAATA
Found at i:10882632 original size:29 final size:29
Alignment explanation
Indices: 10882565--10882640 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
10882555 GCTAAAAAAT
*
10882565 GCCTTTGTGGCACACTCTG-A-ATGAATA
1 GCCTTTGTGGCATACTCTGTATATGAATA
*
10882592 GCC--TATGGCATACTCTGTATAT-ATATA
1 GCCTTTGTGGCATACTCTGTATATGA-ATA
10882619 GCCTTTGTGGCATACTCTGTAT
1 GCCTTTGTGGCATACTCTGTAT
10882641 GGATCGCCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 12 0.29
26 2 0.05
27 11 0.27
29 16 0.39
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (29 bp):
GCCTTTGTGGCATACTCTGTATATGAATA
Found at i:10889870 original size:25 final size:26
Alignment explanation
Indices: 10889842--10889938 Score: 153
Period size: 26 Copynumber: 3.8 Consensus size: 26
10889832 CCTCTTTAAT
**
10889842 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
10889867 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
10889892 AATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
10889918 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
10889939 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 32 0.48
26 35 0.52
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:10890013 original size:20 final size:20
Alignment explanation
Indices: 10889988--10890062 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
10889978 TTATGAATAC
10889988 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10890008 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10890028 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
10890048 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
10890063 ATCCCATGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
18 8 0.15
20 44 0.81
21 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10890019 original size:11 final size:11
Alignment explanation
Indices: 10889988--10890043 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
10889978 TTATGAATAC
10889988 ATCATGTGCAT
1 ATCATGTGCAT
*
10889999 ATCA--TACAT
1 ATCATGTGCAT
10890008 ATCATGTGCAT
1 ATCATGTGCAT
*
10890019 ATCA--TACAT
1 ATCATGTGCAT
10890028 ATCATGTGCAT
1 ATCATGTGCAT
10890039 ATCAT
1 ATCAT
10890044 ATCAATCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:10890060 original size:9 final size:10
Alignment explanation
Indices: 10889988--10890061 Score: 66
Period size: 9 Copynumber: 7.5 Consensus size: 10
10889978 TTATGAATAC
10889988 ATCATGTGCAT
1 ATCATGT-CAT
*
10889999 ATCAT-ACAT
1 ATCATGTCAT
10890008 ATCATGTGCAT
1 ATCATGT-CAT
*
10890019 ATCAT-ACAT
1 ATCATGTCAT
10890028 ATCATGTGCAT
1 ATCATGT-CAT
*
10890039 ATCATATCA-
1 ATCATGTCAT
10890048 ATCATGT-AT
1 ATCATGTCAT
10890057 ATCAT
1 ATCAT
10890062 AATCCCATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
8 1 0.02
9 27 0.52
10 2 0.04
11 22 0.42
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (10 bp):
ATCATGTCAT
Found at i:10898118 original size:25 final size:25
Alignment explanation
Indices: 10898079--10898145 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
10898069 TTAATAACTG
* **
10898079 GGGCAAAGCCATTTTCGGTAAACCA
1 GGGCAAAGCCCTTTTCAATAAACCA
* *
10898104 GGGCAAAACCCTTTTTCAATAAACTA
1 GGGCAAAGCCC-TTTTCAATAAACCA
10898130 GGGCATAAGCCCTTTT
1 GGGCA-AAGCCCTTTT
10898146 GCACTTCCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 9 0.26
26 20 0.59
27 5 0.15
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (25 bp):
GGGCAAAGCCCTTTTCAATAAACCA
Found at i:10898223 original size:20 final size:20
Alignment explanation
Indices: 10898195--10898261 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
10898185 TTATGAATAC
10898195 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
10898215 ATTATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
10898235 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
10898255 ATCATGT
1 ATCATGT
10898262 ATATCAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:10898246 original size:11 final size:11
Alignment explanation
Indices: 10898195--10898250 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
10898185 TTATGAATAC
10898195 ATCATGTGCAT
1 ATCATGTGCAT
*
10898206 ATCA--TACAT
1 ATCATGTGCAT
*
10898215 ATTATGTGCAT
1 ATCATGTGCAT
*
10898226 ATCA--TACAT
1 ATCATGTGCAT
10898235 ATCATGTGCAT
1 ATCATGTGCAT
10898246 ATCAT
1 ATCAT
10898251 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:10898325 original size:25 final size:25
Alignment explanation
Indices: 10898297--10898344 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10898287 ATAAGTAAAC
* * *
10898297 CCTAGGGGTATAACGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
10898322 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
10898345 CATAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:10931907 original size:22 final size:23
Alignment explanation
Indices: 10931859--10931907 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
10931849 ATCCTAACTA
* *
10931859 AATTCACTACTTTTTTTTATCTT
1 AATTCACTACTTTTTTCTATCTC
10931882 AATTCA-TACTTTATTTCTA-CTC
1 AATTCACTACTTT-TTTCTATCTC
10931904 AATT
1 AATT
10931908 TTTAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTCACTACTTTTTTCTATCTC
Found at i:10932333 original size:13 final size:12
Alignment explanation
Indices: 10932311--10932342 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
10932301 ATTCTAATTC
10932311 TTTCTTTTTTTA
1 TTTCTTTTTTTA
10932323 TTTCTTTTTTTA
1 TTTCTTTTTTTA
10932335 TTTACTTT
1 TTT-CTTT
10932343 ACTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTTA
Found at i:10942029 original size:22 final size:23
Alignment explanation
Indices: 10941986--10942032 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
10941976 TGTTTTTAGA
*
10941986 TTTTGAGTAATGAGTTTAATTAT
1 TTTTGAGTAATGAGTATAATTAT
10942009 TTTTGAGTTAATGA-TAT-ATTAT
1 TTTTGAG-TAATGAGTATAATTAT
10942031 TT
1 TT
10942033 AACATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 9 0.41
24 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (23 bp):
TTTTGAGTAATGAGTATAATTAT
Found at i:10944522 original size:20 final size:21
Alignment explanation
Indices: 10944493--10944550 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 21
10944483 AAAAAATTAT
*
10944493 AAAAACTATTTTTAAAA-ACA
1 AAAAATTATTTTTAAAATACA
** *
10944513 AAAAATTA-TTGAAAAATATA
1 AAAAATTATTTTTAAAATACA
*
10944533 AAAAATTATTTTTTAAAT
1 AAAAATTATTTTTAAAAT
10944551 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTATTTTTAAAATACA
Found at i:10947638 original size:19 final size:21
Alignment explanation
Indices: 10947604--10947644 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
10947594 ATTTTTATAC
*
10947604 ATTTACATTATAATATAGTAT
1 ATTTACATTATAATATAATAT
10947625 ATTTA-ATT-TAATATAATAT
1 ATTTACATTATAATATAATAT
10947644 A
1 A
10947645 AATTATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTACATTATAATATAATAT
Found at i:10954320 original size:26 final size:26
Alignment explanation
Indices: 10954291--10954342 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10954281 ATAGTATGAG
10954291 TTTCATAAAAAATGGCAAATAATTCT
1 TTTCATAAAAAATGGCAAATAATTCT
10954317 TTTCATAAAAAATGGCAAATAATTCT
1 TTTCATAAAAAATGGCAAATAATTCT
10954343 ATGTAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (26 bp):
TTTCATAAAAAATGGCAAATAATTCT
Found at i:10955066 original size:55 final size:55
Alignment explanation
Indices: 10954928--10955066 Score: 152
Period size: 55 Copynumber: 2.5 Consensus size: 55
10954918 AAGGTCCACA
* **
10954928 CCCGTGTTGTTTTGGCAGGTTTGCCCACGGTTGCTTGGCACGGGCATGTCACACG
1 CCCGTGTTGTTTTGGCAGGTTCGCCCACGGTTGCAAGGCACGGGCATGTCACACG
** * * * ** *
10954983 CCCGTGTTAATTTGACAGGTTCGGCCACGGTTTCAAGGCACGGGTGTGTCGCACG
1 CCCGTGTTGTTTTGGCAGGTTCGCCCACGGTTGCAAGGCACGGGCATGTCACACG
* * *
10955038 CCCGTGTTGTTTTGGTAGCTTCACCCACG
1 CCCGTGTTGTTTTGGCAGGTTCGCCCACG
10955067 ACCATGTCGC
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.13, C:0.27, G:0.31, T:0.29
Consensus pattern (55 bp):
CCCGTGTTGTTTTGGCAGGTTCGCCCACGGTTGCAAGGCACGGGCATGTCACACG
Found at i:10965754 original size:30 final size:30
Alignment explanation
Indices: 10965720--10965780 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
10965710 CATTTAATAC
10965720 AAACTTTGGAAAAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
10965750 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
10965780 A
1 A
10965781 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:10969801 original size:46 final size:46
Alignment explanation
Indices: 10969749--10970011 Score: 368
Period size: 46 Copynumber: 5.7 Consensus size: 46
10969739 ATGCCATATG
* * * *
10969749 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCATGCTGCCATGGTA
** *
10969795 TCTTTCAACCATGGTCTTATTCATTTCATGTCATGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTA
* *
10969841 TCTTTCAACCATGGTCTTACACATTTTATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTA
*
10969887 TCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTA
* * *
10969933 TCTTTCAACCATGGTCTTACACATTTCATA-AATGGTTGTCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAT-GCTGCCATGGTA
*
10969979 TCTTTCAACCATGGTCATACACATTTCATATCA
1 TCTTTCAACCATGGTCTTACACATTTCATATCA
10970012 GAGAGCACAC
Statistics
Matches: 199, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
45 5 0.03
46 193 0.97
47 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCATGCTGCCATGGTA
Found at i:10972460 original size:30 final size:30
Alignment explanation
Indices: 10972424--10972483 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
10972414 TTCTCGAGCC
10972424 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
* *
10972454 TAGGGGCAAAAGTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
10972484 CGTATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATGCAAAAGTT
Found at i:10972961 original size:46 final size:46
Alignment explanation
Indices: 10972905--10973257 Score: 706
Period size: 46 Copynumber: 7.7 Consensus size: 46
10972895 TGGTTGAGCA
10972905 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10972951 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10972997 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10973043 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10973089 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10973135 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10973181 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
10973227 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
10973258 TTAGGGGCGG
Statistics
Matches: 307, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 307 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:10974018 original size:59 final size:58
Alignment explanation
Indices: 10973926--10974042 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 58
10973916 CAGAATATTG
*
10973926 CTGCAGCAATGACATGAATTTTAAAAATCACTAAAAATAGTATAAATGGAACTAAATAA
1 CTGCAGCAATGACATGAATTTGAAAAATCACT-AAAATAGTATAAATGGAACTAAATAA
10973985 CTGCAGCAATGACATGAATTTGAAAAATCACTAAAATAGTATAAATGGAACTAAATAA
1 CTGCAGCAATGACATGAATTTGAAAAATCACTAAAATAGTATAAATGGAACTAAATAA
10974043 TGAGTAAGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 26 0.46
59 31 0.54
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (58 bp):
CTGCAGCAATGACATGAATTTGAAAAATCACTAAAATAGTATAAATGGAACTAAATAA
Found at i:10976446 original size:51 final size:51
Alignment explanation
Indices: 10976382--10976517 Score: 173
Period size: 51 Copynumber: 2.7 Consensus size: 51
10976372 TGGAAACATG
* *
10976382 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * * * ** *
10976433 ATCTTATAAGATATTATTTTATAATATTACATATCTTATCTAAGATATGTA
1 ATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
*
10976484 ATCTTATAAGATATGATATTATATTCTTAGAGAT
1 ATCTTATAAGATATGATATTATAATCTTAGAGAT
10976518 TTGATGGTAG
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.43
Consensus pattern (51 bp):
ATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:10976495 original size:17 final size:17
Alignment explanation
Indices: 10976425--10976498 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
10976415 TCTTAGATAT
*
10976425 GATATGGAATCTTATAA
1 GATATGTAATCTTATAA
*
10976442 GATAT-T-ATTTTATAA
1 GATATGTAATCTTATAA
* **
10976457 TAT-TACATATCTTATCTAA
1 GATATGTA-ATCTTA--TAA
10976476 GATATGTAATCTTATAA
1 GATATGTAATCTTATAA
10976493 GATATG
1 GATATG
10976499 ATATTATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
14 1 0.02
15 10 0.23
17 19 0.44
19 11 0.26
20 2 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (17 bp):
GATATGTAATCTTATAA
Found at i:10978371 original size:96 final size:96
Alignment explanation
Indices: 10978200--10978489 Score: 454
Period size: 96 Copynumber: 3.0 Consensus size: 96
10978190 GTGTCCGAGG
* * * * * *
10978200 AAGTCTGTTATCGATGGGAATGATCGAGCAGATACGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATAGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
* *
10978265 AAAAGTCGAAGCCAAGAGGGCAAAGAGGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
* *
10978296 AAGTCTGTCATCGAAGGGAACGATGGAGCAGACCAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATAGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
10978361 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
* * *
10978392 AAGTCTGTCATCAAAGGAAACGATAGAGTAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
1 AAGTCTGTCATCGAAGGGAACGATAGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
*
10978457 TAAAGCCGAAGCCAAGAGGGCTAAGAGGAGC
66 TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
10978488 AA
1 AA
10978490 AAAGAAGCGA
Statistics
Matches: 179, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 179 1.00
ACGTcount: A:0.36, C:0.18, G:0.34, T:0.12
Consensus pattern (96 bp):
AAGTCTGTCATCGAAGGGAACGATAGAGCAGACAAGGAGCCCAAGAAGCTTGGTTCGAGCAAGGG
TAAAGCCGAAGCCAAGAGGGCAAAGAGGAGC
Found at i:10979460 original size:51 final size:51
Alignment explanation
Indices: 10979396--10979531 Score: 164
Period size: 51 Copynumber: 2.7 Consensus size: 51
10979386 TGGAAACATG
*
10979396 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGGA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* * * * * * ** *
10979447 ATCTTATAAGATATTATTTTATAATATTACATATCTTATCTAAGATATGTA
1 ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
* *
10979498 ATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 ATCTTAAAAGATATGATATTATAATCTTAGAGAT
10979532 TTGATGGTAG
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (51 bp):
ATCTTAAAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGGA
Found at i:10984004 original size:30 final size:30
Alignment explanation
Indices: 10983968--10984027 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
10983958 TTCCCGAGCC
10983968 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
* *
10983998 TAGGGGCAAAAGTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
10984028 CGTATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATGCAAAAGTT
Found at i:10985015 original size:42 final size:42
Alignment explanation
Indices: 10984953--10985035 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
10984943 TCGATCACAC
10984953 TATCCAAAGGACTTTCATCTGGGTAAATGGCTTGTAAAACTG
1 TATCCAAAGGACTTTCATCTGGGTAAATGGCTTGTAAAACTG
*
10984995 TATCCAAAGGACTTTTATCTGGGTAAATGGCTTGTAAAACT
1 TATCCAAAGGACTTTCATCTGGGTAAATGGCTTGTAAAACT
10985036 TAAGTATGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (42 bp):
TATCCAAAGGACTTTCATCTGGGTAAATGGCTTGTAAAACTG
Done.